Inverse (or reverse) docking approach which involves docking of a ligand against a set of
protein structures to predict possible protein target(s), possess limitations, including inefficient
empirical scoring schemes and similarities in protein active site shape and physico-chemical
properties. To overcome this limitation, we combined receptor- and ligand-based methods to predict
probable protein targets. We showed that the experimental protein target along with possible offtargets
can be effectively retrieved if the docking energy of the reference molecule and probe
molecules based scaled energy profiles were combined and clustered together. The present method
was validated using 7,8-dialkyl-1,3-diaminopyrrolo[3,2-f]quinazolines that inhibit Candida albicans dihydrofolate
reductase (DHFR) in vitro.
Keywords: Inverse docking, molecular modeling, pharmacophore analysis, scoring schemes, structure-activity relationships.
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